In order to support the goals and of the CHAIN Center and its investigators advanced mass spectrometric based analyses are needed. The aims proposed in the CHAIN Center cover a broad range of critical topics including biomarker discovery, assessment of the role of macrophages in neuronal damage, and the need for CNS penetrating antiviral drugs. These invesfigations are planned in order to advance our knowledge, prevention and treatment of neuroAIDS in the now chronic setting of HIV infection, and its relationship to aging. Here we will provide state of the art proteomic and metabolomics technologies to enable the identification, quantification, and correlation of the broad range of proteins and metabolites relevant to neuroAIDS. Meeting this challenge is integral to understanding the now altered progression of disease and the development of diagnostic and treatment tools. Our methods and analyses will permit the identification of specific proteins and metabolites associated with neuroAIDS and its models. One of expectations is that results of proteomics experiments will be integrated with metabolomics data, and through the use of analysis tools in this Core, the Bioinformatics subunit of the Administrative Core and the Systems Biology Core a collaborative effort will result in integrated data collection, sharing and analysis capabilities that are simultaneously divers and integrated, not only enabling our investigators to meet their scientific aims but generating a unique resource for neuroAIDS. This will be accomplished within the Core and Center as a whole and is directly applicable to in vitro, in vivo and ex vivo clinical translational studies performed in the examination of the effects of HIV on the CNS. The Specific Aims are designed to meet the Center's Action Plan, and the two Core Directors not only bring significant expertise in proteomics and metabolomics but also have a good understanding of HIV and its neurobiology, and experience in neuroAIDS studies, which facilitate the likelihood of success of CHAIN Center investigators. Analytical instrumentation and scientific capabilities are complementary among proteomics and metabolomics components of this Core. Both directors will promote and facilitate communication between the CHAIN Center investigators and the cores to insure that the most optimal experimental approaches and instrumentation will be used.